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In this paper, a series of equilibrium molecular dynamics simulations (EMD), steered molecular dynamics (SMD), and computational electrophysiology methods are carried out to explore water and ion permeation through mechanosensitive channels of large conductance (MscL). This research aims to identify the pore-lining side chains of the channel in different conformations of MscL homologs by analyzing the pore size. The distribution of permeating water dipole angles through the pore domains enclosed by VAL21 and GLU104 demonstrated that water molecules are oriented toward the charged oxygen headgroups of GLU104 from their hydrogen atoms to retain this interaction in a stabilized fashion. Although, this behavior was not perceived for VAL21. Numerical assessments of the secondary structure clarified that, during the ion permeation, in addition to the secondary structure alterations, the structure of Tb-MscL would also undergo significant conformational changes. It was elucidated that VAL21, GLU104, and water molecules accomplish a fundamental task in ion permeation. The mentioned residues hinder ion permeation so that the pulling SMD force is increased remarkably when the ions permeate through the domains enclosed by VAL21 and GLU102. The hydration level and potassium diffusivity in the hydrophobic gate of the transmembrane domain were promoted by applying the external electric field. Furthermore, the implementation of an external electric field altered the distribution pattern for potassium ions in the system while intensifying the accumulation of Cl

A new solvent stimuli-responsive metallogel (VGel) was synthesized through the introduction of vanadium ions into an adenine (Ade) and 1,3,5-benzene tricarboxylic acid (BTC) organogel, and its supramolecular self-assembly was investigated from a computational viewpoint. A relationship between the synthesized VGel integrity and the self-assembly of its components is demonstrated by a broad range of molecular dynamics (MD) simulations, an aspect that has not yet been explored for such a complex metallogel in particular. MD simulations and Voronoi tessellation assessments, both in agreement with experimental data, confirm the gel formation. Based on excellent water stability and the ethanol/methanol stimuli-responsive feature of the VGel an easy-to-use visualization assay for the detection of counterfeit liquor with a 6% (v/v) methanol limit of detection in 40% (v/v) ethanol is reported. These observations provide a cheap and technically simple method and are a step towards the immersible screening of similar molecules in methanol-spiked beverages.

In this study, adsorption of water nanodroplets, oil nanodroplets and oil–water mixtures on a poly vinylidene fluoride (PVDF) surface is investigated computationally by a molecular dynamics (MD) approach and a mechanism for adsorption of the droplets is proposed. MD simulation results revealed that the PVDF surface is hydrophobic and oleophilic and can be used to separate oil from water. The acquired results are in good agreement with experimental results. As to investigate the origins for hydrophobicity of the PVDF surface, mobility of water molecules on the PVDF surface has been meticulously investigated. Investigations have proven that once the water molecules are organized singly or in small groups with two or three molecules, they exhibit very low levels of mobility, whereas water molecules in groups of four or more have high mobility. Some descriptive studies were performed based on MD simulation results to investigate the behavior observed in the systems including: (i) distribution of partial charges on the surface of PVDF. (ii) Dependence of the orientation of water molecules near the PVDF surface on the size of water cluster. (iii) Dependence of the distance of water molecules to the PVDF surface on the water cluster size. Manner of charge distribution on the PVDF demonstrated a formation of nano-domains with positive and negative charges on the surface. Dependence of the behavior of water molecules on the nano-domains on the water cluster size was investigated.

We present an investigation on the permeability and selectivity of graphene sheets with designed sub nanometer pores using molecular dynamics simulations. We show that nanoporous graphene can be used to separate water from a gaseous mixture of nitrogen, oxygen and water. The obtained results show that the separation is performed based on the absorption of water molecules on the nanoporous graphene surface. Pore size plays an important role in the possible formation of water clusters on the nanoporous graphene surface. In graphene sheets with large pores, the space between the neighboring graphene becomes smaller and water molecules form a cluster on the graphene surface quickly. Because the size of the water clusters is larger than that of the nanopore, they cannot pass through it, whereas nitrogen and oxygen molecules are able to pass through the nanoporous graphene. In this study, we propose a mechanism for the formation of water clusters on the nanoporous graphene surface. To illustrate the different steps of the proposed mechanism, several investigations were performed such as calculation of the distribution and accumulation of water molecules on the graphene surface, angle between the dipolar moment vector of water molecules and the graphene surface and formation and movement of multi-layer clusters. Moreover, a specific method to pass N2 and O2 molecules through nanoporous graphene is presented.

In this work, we compared the structural and dynamical properties of water confined between two graphene oxide (GO) sheets with water confined between two graphene sheets through molecular dynamics simulations. Our results showed how the structure and dynamics of the water near the GO surfaces changes under confinement conditions. Different orientations of the water molecules to the GO sheets confirm the heterogeneous nature of the confined water. The density distribution of water near the GO sheets is different from the graphene surfaces due to the presence of hydrophilic functional groups of the GO sheets. Also, the hydrogen bonds between the water molecules are disturbed due to the presence of these groups on the GO surfaces. The results showed that as water molecules in areas which are close to the GO surfaces are isolated, and due to hydrogen bond formation between water molecules and the substituents of the GO, the water molecules have fewer hydrogen bonds with other water molecules around. In the middle region between two GO sheets, it has been seen that each water molecule is surrounded by more water molecules, and there are many more hydrogen bonds, so it is possible to consider a network structure of water in this region. There is a good quantitative agreement between experiments and the above mentioned results. These results were confirmed by the calculated coordination number, radial distribution functions and mean square displacements.

In this work, the liquid–solid phase transition temperature of water confined between two graphene oxide (GO) sheets is investigated using molecular dynamics simulations. The results demonstrate that, due to the presence of functional groups of the GO sheets, at temperatures below liquid–solid phase transition temperature, the water molecules near the confining sheets are not structured like ice and remained in the liquid form. The results also reveal the confinement effects on the melting and freezing rate of water molecules. The confining conditions delay the freezing process of the water molecules compared to the bulk water molecules. These results are confirmed by the calculated total energy, the density profile of water molecules confined between two GO sheets, the number of hydrogen bonding, radial distribution function, and mean square displacement. The liquid–solid phase transition temperature of water in the presence of GO sheets was calculated as 236 K, which was 34 K less than the temperature of the bulk water.